private IEnumerable<TagMatch> FindMatchesWithFeatureMass(MatchedTag matchedTag)
{
if (matchedTag.NTermFlankingMass == null || matchedTag.CTermFlankingMass == null) yield break;
var featureMass = (double) matchedTag.NTermFlankingMass + matchedTag.Mass +
(double)matchedTag.CTermFlankingMass + Composition.H2O.Mass;
var shiftMass = matchedTag.Mass + (double)matchedTag.NTermFlankingMass;
var backwardGraph = new ShiftedSequenceGraph(_aaSet, shiftMass, false,
matchedTag.StartIndex, featureMass - MinSumModificationMasses);
foreach (var backwardMatch in GetBackwardMatches(matchedTag, backwardGraph, featureMass))
{
// Make a forward graph
var nTermShiftMass = backwardMatch.Mass + matchedTag.Mass;
var forwardGraph = new ShiftedSequenceGraph(_aaSet, nTermShiftMass, true,
_proteinSequence.Length - matchedTag.EndIndex, featureMass - MinSumModificationMasses);
foreach (
var forwardMatch in
GetForwardMatches(matchedTag, forwardGraph, featureMass))
{
var mass = forwardMatch.Mass + matchedTag.Mass + backwardMatch.Mass;
if (mass > _maxSequenceMass) continue;
var offset = matchedTag.EndIndex - backwardMatch.Index - 1;
var modStr = string.Join(",", backwardMatch.Modifications.Concat(forwardMatch.Modifications.Select(m => m.GetModificationInstanceWithOffset(offset))));
var modList = new List<Modification>();
foreach (var mod in backwardMatch.Modifications) modList.Add(mod.Modification);
foreach (var mod in forwardMatch.Modifications) modList.Add(mod.Modification);
var tagMatch = new TagMatch(
backwardMatch.Index,
forwardMatch.Index,
matchedTag.Length,
backwardMatch.Charge,
backwardMatch.Score,
forwardMatch.Score,
mass,
new ModificationCombination(modList),
modStr);
yield return tagMatch;
}
}
}
private IEnumerable<FlankingMassMatch> GetBackwardMatches(
MatchedTag matchedTag,
ShiftedSequenceGraph backwardGraph,
double? featureMass = null
)
{
for (var j = matchedTag.StartIndex - 1; j >= -1; j--)
{
var residue = j >= 0 ? _proteinSequence[j] : AminoAcid.ProteinNTerm.Residue;
var location = j > 0 ? SequenceLocation.Everywhere : SequenceLocation.ProteinNTerm;
if(!backwardGraph.AddAminoAcid(residue, location)) yield break;
if (j == 0) continue;
var backwardMatch = GetBestMatchInTheGraph(backwardGraph, _spec, featureMass);
if (backwardMatch != null)
{
backwardMatch.Index = Math.Max(j, 0);
yield return backwardMatch;
}
}
}
private FlankingMassMatch GetBestMatchInTheGraph(ShiftedSequenceGraph seqGraph, ProductSpectrum spec, double? featureMass)
{
FlankingMassMatch match = null;
var bestScore = double.NegativeInfinity;
var protCompositions = seqGraph.GetSequenceCompositions();
for (var modIndex = 0; modIndex < protCompositions.Length; modIndex++)
{
seqGraph.SetSink(modIndex);
var protCompositionWithH2O = seqGraph.GetSinkSequenceCompositionWithH2O();
var sequenceMass = protCompositionWithH2O.Mass;
if (featureMass != null && !_tolerance.IsWithin(sequenceMass, (double)featureMass)) continue;
var charge =
(int)
Math.Round(sequenceMass /
(spec.IsolationWindow.IsolationWindowTargetMz - Constants.Proton));
var mostAbundantIsotopeMz = Ion.GetIsotopeMz(sequenceMass, charge,
Averagine.GetIsotopomerEnvelope(sequenceMass).MostAbundantIsotopeIndex);
if (!spec.IsolationWindow.Contains(mostAbundantIsotopeMz)) continue;
//var feature = new TargetFeature(sequenceMass, charge, spec.ScanNum);
if (_featureFinder != null)
{
var ms1Corr = _featureFinder.GetMs1EvidenceScore(spec.ScanNum, sequenceMass, charge);
if (ms1Corr < Ms1CorrThreshold) continue;
}
var curScoreAndModifications = seqGraph.GetScoreAndModifications(_ms2Scorer);
var curScore = curScoreAndModifications.Item1;
// var curScore = seqGraph.GetFragmentScore(_ms2Scorer);
if (curScore > bestScore)
{
match = new FlankingMassMatch(curScore,
sequenceMass - Composition.H2O.Mass - seqGraph.ShiftMass, charge, curScoreAndModifications.Item2);
//match = new FlankingMassMatch(curScore,
// sequenceMass - Composition.H2O.Mass - seqGraph.ShiftMass, charge, new ModificationInstance[0]);
bestScore = curScore;
}
}
return match;
}
// private readonly int _minProductIonCharge;
// private readonly int _maxProductIonCharge;
private IEnumerable<FlankingMassMatch> GetForwardMatches(
MatchedTag matchedTag,
ShiftedSequenceGraph forwardGraph,
double? featureMass = null
)
{
for (var i = matchedTag.EndIndex; i <= _proteinSequence.Length; i++)
{
var residue = i < _proteinSequence.Length ? _proteinSequence[i] : AminoAcid.ProteinCTerm.Residue;
var location = i < _proteinSequence.Length - 1
? SequenceLocation.Everywhere
: SequenceLocation.ProteinCTerm;
if (!forwardGraph.AddAminoAcid(residue, location)) yield break;
if (i == _proteinSequence.Length - 1) continue;
var forwardMatch = GetBestMatchInTheGraph(forwardGraph, _spec, featureMass);
if (forwardMatch != null)
{
forwardMatch.Index = Math.Min(i + 1, _proteinSequence.Length);
yield return forwardMatch;
}
}
}
